At a glance

This report contains visualisations of alignment statistics for paired tumor/normal samples that can help in understanding the results from wf-somatic-variation. Each section contains different plots or tables. You can quickly jump to an individual section with the links in the header bar.

Tumor Total Reads

1781909

Normal Total Reads

293794

Tumor Read N50

8349 bp

Normal Read N50

7094 bp

Tumor mean coverage

2.471x

Normal mean coverage

0.365x

Base statistics

The aligned bam files have been tested for coverage thresholds of 20.0x for the tumor and 20.0x for the normal sequences.

Sample Type Total Reads Median Read Length Read N50 Min chrom. coverage Mean chrom. coverage Max chrom. coverage Pass threshold
SAMPLE Tumor 1781909 2316 8349 0.243 2.471 1068.097 FAIL
SAMPLE Normal 293794 2149 7094 0.044 0.365 135.737 FAIL

Read statistics

ref sample_name total primary secondary supplementary unmapped qcfail duplicate duplex duplex_forming status
chr1 SAMPLE 203103 154718 47406 979 0 0 0 0 0 Mapped
chr2 SAMPLE 164158 139228 24027 903 0 0 0 0 0 Mapped
chr3 SAMPLE 170717 157546 12071 1100 0 0 0 0 0 Mapped
chr4 SAMPLE 140735 97365 42338 1032 0 0 0 0 0 Mapped
chr5 SAMPLE 138972 107662 30217 1093 0 0 0 0 0 Mapped
chr6 SAMPLE 123550 112761 10163 626 0 0 0 0 0 Mapped
chr7 SAMPLE 97158 83539 13013 606 0 0 0 0 0 Mapped
chr8 SAMPLE 96925 86531 9875 519 0 0 0 0 0 Mapped
chr9 SAMPLE 115621 81612 33272 737 0 0 0 0 0 Mapped
chr10 SAMPLE 107110 80663 25806 641 0 0 0 0 0 Mapped
chr11 SAMPLE 90289 79815 9937 537 0 0 0 0 0 Mapped
chr12 SAMPLE 97465 91401 5498 566 0 0 0 0 0 Mapped
chr13 SAMPLE 67726 62914 4497 315 0 0 0 0 0 Mapped
chr14 SAMPLE 61391 56221 4847 323 0 0 0 0 0 Mapped
chr15 SAMPLE 65749 50386 15011 352 0 0 0 0 0 Mapped
chr16 SAMPLE 74332 53124 20551 657 0 0 0 0 0 Mapped
chr17 SAMPLE 68847 47584 20842 421 0 0 0 0 0 Mapped
chr18 SAMPLE 40179 34011 5918 250 0 0 0 0 0 Mapped
chr19 SAMPLE 46646 31034 15255 357 0 0 0 0 0 Mapped
chr20 SAMPLE 72287 50944 20814 529 0 0 0 0 0 Mapped
chr21 SAMPLE 46345 25059 20927 359 0 0 0 0 0 Mapped
chr22 SAMPLE 29474 17597 11311 566 0 0 0 0 0 Mapped
chrM SAMPLE 5966 4931 19 1016 0 0 0 0 0 Mapped
chrX SAMPLE 70922 61774 8709 439 0 0 0 0 0 Mapped
chrY SAMPLE 12716 2514 9838 364 0 0 0 0 0 Mapped
* SAMPLE 10975 0 0 0 10975 0 0 0 0 Unmapped
ref sample_name total primary secondary supplementary unmapped qcfail duplicate duplex duplex_forming status
chr1 SAMPLE 36928 25488 11203 237 0 0 0 0 0 Mapped
chr2 SAMPLE 27037 23772 3113 152 0 0 0 0 0 Mapped
chr3 SAMPLE 19985 17330 2537 118 0 0 0 0 0 Mapped
chr4 SAMPLE 19672 13352 6197 123 0 0 0 0 0 Mapped
chr5 SAMPLE 24653 18196 6292 165 0 0 0 0 0 Mapped
chr6 SAMPLE 22056 18964 2999 93 0 0 0 0 0 Mapped
chr7 SAMPLE 22941 18974 3830 137 0 0 0 0 0 Mapped
chr8 SAMPLE 12589 11035 1493 61 0 0 0 0 0 Mapped
chr9 SAMPLE 19067 13036 5849 182 0 0 0 0 0 Mapped
chr10 SAMPLE 17863 13885 3868 110 0 0 0 0 0 Mapped
chr11 SAMPLE 16092 13657 2364 71 0 0 0 0 0 Mapped
chr12 SAMPLE 17370 14662 2610 98 0 0 0 0 0 Mapped
chr13 SAMPLE 9290 7675 1573 42 0 0 0 0 0 Mapped
chr14 SAMPLE 10882 9065 1775 42 0 0 0 0 0 Mapped
chr15 SAMPLE 7629 6064 1531 34 0 0 0 0 0 Mapped
chr16 SAMPLE 12223 9154 3016 53 0 0 0 0 0 Mapped
chr17 SAMPLE 15659 10874 4706 79 0 0 0 0 0 Mapped
chr18 SAMPLE 9686 6942 2685 59 0 0 0 0 0 Mapped
chr19 SAMPLE 11017 7013 3951 53 0 0 0 0 0 Mapped
chr20 SAMPLE 13144 9409 3645 90 0 0 0 0 0 Mapped
chr21 SAMPLE 8886 5094 3722 70 0 0 0 0 0 Mapped
chr22 SAMPLE 8133 4881 3133 119 0 0 0 0 0 Mapped
chrM SAMPLE 740 622 3 115 0 0 0 0 0 Mapped
chrX SAMPLE 11646 9603 1984 59 0 0 0 0 0 Mapped
chrY SAMPLE 2562 556 1913 93 0 0 0 0 0 Mapped
* SAMPLE 4491 0 0 0 4491 0 0 0 0 Unmapped

Coverage

Depth of coverage computed by mosdepth. The dashed line shows the total mean coverage.

Software versions

Name Version
python 3.8.19
samtools 1.19.2
fastcat 0.18.6
ezcharts 0.11.2
pysam 0.22.0
bgzip 1.19.1
tabix 1.19.1
minimap2 2.24-r1122
mosdepth 0.3.3
bedtools v2.31.0

Workflow parameters

Key Value
sv True
mod False
snv False
bam_normal data/input/bam_normal/sorted-indexed_MMNK-1.bam
bam_tumor data/input/bam_tumor/sorted-indexed_KKU-213A.bam
sample_name SAMPLE
ref data/input/ref/GRCh38_reference.fa
bed None
tr_bed None
annotation True
out_dir outputs/out_dir/
ubam_map_threads 8
ubam_sort_threads 3
ubam_bam2fq_threads 1
tumor_min_coverage 20
normal_min_coverage 20
depth_window_size 50000
depth_intervals False
override_basecaller_cfg None
normal_vcf None
hybrid_mode_vcf None
genotyping_mode_vcf None
skip_haplotype_filter False
haplotype_filter_threads 4
ctg_name EMPTY
include_all_ctgs False
snv_min_af 0.05
indel_min_af 0.05
min_contig_size 0
min_qual 8
min_cov 4
min_bq None
use_longphase True
use_longphase_intermediate True
use_normal_hets_for_phasing True
use_tumor_hets_for_phasing False
use_het_indels_for_phasing True
use_longphase_haplotag True
liquid_tumor False
print_ref_calls False
print_germline_calls False
germline True
phase_normal False
clairs_debug False
fast_mode False
clair3_base_err 0.001
clair3_gq_bin_size 5
clair3_phase_vcf False
clair3_ref_pct_full 0.1
clair3_var_pct_full 0.7
clair3_min_mq 5
GVCF False
vcf_fn EMPTY
clairs_to_qual 12
clairs_to_min_bq 20
qual_cutoff_phaseable_region 14
qual_cutoff_unphaseable_region 20
severus_threads 8
min_sv_length 50
min_support 3
vaf_threshold None
severus_args None
force_strand False
modkit_args None
diff_mod True
dss_threads 1
modkit_threads 4
igv True